Question About Malwarebytes..somebody please help.

I installed Malwarebytes from their official website and after it downloaded, I double clicked on the waterfox little downloadbox and then run and set it up that way. But after everythings done, I closed it and then I now double clicked on the Malwarebytes icon on the desktop and Windows asked me "Are you sure you want to make changes to this computer?" or said something like that. The thing is I already clicked "Yes" for that same question when double clicking on that program from the Waterfox download box. What should I do? Is it still safe to click "yes" even though I already clicked "yes" before?

We just scanned and found a trojan in the temp files which we removed and sent to quarantine, only problem is its NOT in the quarantine. Is there anyway we can find where it put it since we did see it say deleted and quarantined successfully.

Oh ok. Is there any way I could disable the cookies on that program when scanning? Also, which option should I choose for PUP for scanning under settings section?

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I do not believe MBAM creates cookies when it scans. What I think you mean is that you are asking if you can disable MBAM from scanning cookies. MBAM does not scan cookies. You can leave it as it is for PUP.

We just scanned and found a trojan in the temp files which we removed and sent to quarantine, only problem is its NOT in the quarantine. Is there anyway we can find where it put it since we did see it say deleted and quarantined successfully.

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Well, I have no idea. It would be a good idea to scan the system again. I believe temp files pose no threat to the system, however.

After I put a check next to the threat that was detected, I clicked on quarantine but then it said it has been moved to quarantine and has been deleted successfully. Is there any way it can stay in quarantine and not have the file(s) deleted? I do not want to delete ANY files if there is any FP's. Also, everytime when I click on the Malwarebytes icon on my desktop, Windows always asks me "Are you sure you want to make changes to this computer?" whenever I click on that icon.

After I put a check next to the threat that was detected, I clicked on quarantine but then it said it has been moved to quarantine and has been deleted successfully. Is there any way it can stay in quarantine and not have the file(s) deleted? I do not want to delete ANY files if there is any FP's. Also, everytime when I click on the Malwarebytes icon on my desktop, Windows always asks me "Are you sure you want to make changes to this computer?" whenever I click on that icon.

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It is normal because it requires elevated privileges to run. You can't do that. If you believe it is a false positive, you can always restore it from the quarantine.

Nothing is in the quarantine. After the scan we hit remove, it said deleting and quarantined and we went to check on it and it was empty, nothing was there. How can we prevent this in the future? Also why wasn't it in quarantine when it SAID it put it there?

It is normal because it requires elevated privileges to run. You can't do that. If you believe it is a false positive, you can always restore it from the quarantine.

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The problem is it wont let me keep it in quarantine box..after I clicked remove and quarantine, it quarantined it and then deleted it. I couldn't find it under settings in order to keep a file quarantined and not to delete files.

Nothing is in the quarantine. After the scan we hit remove, it said deleting and quarantined and we went to check on it and it was empty, nothing was there. How can we prevent this in the future? Also why wasn't it in quarantine when it SAID it put it there?

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Well, I do not know what happened that
Maybe you can check the logs to see what happened.

The problem is it wont let me keep it in quarantine box..after I clicked remove and quarantine, it quarantined it and then deleted it. I couldn't find it under settings in order to keep a file quarantined and not to delete files.

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There is no such option. If you are sure it is malware delete it. If you are unsure, leave it in the quarantine and look it up, and if it is safe you can always restore from quarantine.